With the increase of world population, rice production has to be doubled by 2050 2. Rice is a major food crop for over half of the world population, accounting for almost 90% of production of global rice by Asian countries 1.
Pyramided recombinant inbred lines provide a valuable source for integration into future breeding programs.
The results indicate that this new population has enabled identifications of significant QTLs and interactions for 16 traits through multiple approaches. Moreover, we identified a number of candidate QTLs in either one or two analyses but further validations will be needed. Notably, nine known QTLs/genes qPH 1/ OsGA20ox2, qDF 3/ OsMADS50, PL, QDg1, qGW-5b, grb7-2, qGL 3/ GS3, Amy6/ Wx gene and OsNAS3 were consistently identified by all approaches for nine traits whereas qDF 3/ OsMADS50 was co-located for both yield and days-to-flowering traits on chromosome 3. Genome-wide association study and interval mapping identified 38 and 34 QTLs whereas Bayesian networking detected 60 QTLs with 22 marker-marker associations, 32 trait-trait associations and 65 marker-trait associations. In this study we report advantages of using Multi-parent Advanced Generation Inter-Crosses global population, derived from a combination of eight indica and eight japonica elite parents, in QTL discovery for yield and grain quality traits. Most of QTL mapping studies were carried out from crosses made within the subspecies, either indica × indica or japonica × japonica. Identification of Quantitative Trait Loci (QTL) has been a challenge for complex traits due to the use of populations with narrow genetic base.
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